scholarly journals Spliceosomal snRNA Epitranscriptomics

2021 ◽  
Vol 12 ◽  
Author(s):  
Pedro Morais ◽  
Hironori Adachi ◽  
Yi-Tao Yu
Keyword(s):  
Cell Nucleus ◽  
Current Knowledge ◽  
Protein Complexes ◽  
Mrna Splicing ◽  
Rna Modifications ◽  
Small Nuclear Rnas ◽  
Sequence Elements ◽  
Critical Components ◽  
Rna Protein Complexes ◽  
Small Nuclear Ribonucleoproteins

Small nuclear RNAs (snRNAs) are critical components of the spliceosome that catalyze the splicing of pre-mRNA. snRNAs are each complexed with many proteins to form RNA-protein complexes, termed as small nuclear ribonucleoproteins (snRNPs), in the cell nucleus. snRNPs participate in pre-mRNA splicing by recognizing the critical sequence elements present in the introns, thereby forming active spliceosomes. The recognition is achieved primarily by base-pairing interactions (or nucleotide-nucleotide contact) between snRNAs and pre-mRNA. Notably, snRNAs are extensively modified with different RNA modifications, which confer unique properties to the RNAs. Here, we review the current knowledge of the mechanisms and functions of snRNA modifications and their biological relevance in the splicing process.

Nuclear import of spliceosomal snRNPsThis paper is one of a selection of papers published in this Special Issue, entitled The Nucleus: A Cell Within A Cell.

2006 ◽  
Vol 84 (3-4) ◽  
pp. 367-376 ◽  
Author(s):  
Christiane Rollenhagen ◽  
Nelly Panté
Keyword(s):  
Cell Nucleus ◽  
Nuclear Import ◽  
Current Knowledge ◽  
Protein Complexes ◽  
Special Issue ◽  
A Cell ◽  
Rna Maturation ◽  
Small Nuclear Ribonucleoproteins ◽  
Selection Of

Uridine-rich small nuclear ribonucleoproteins (U snRNPs) are the building units of the spliceosome. These RNA and protein complexes assemble in the cytoplasm. After proper assembly and RNA maturation, mature U snRNPs are imported into the cell nucleus, where they take part in the splicing process. In this paper we review the current knowledge of how U snRNPs enter the nucleus.

scholarly journals U4 small nuclear RNA dissociates from a yeast spliceosome and does not participate in the subsequent splicing reaction.

1991 ◽  
Vol 11 (11) ◽  
pp. 5571-5577 ◽  
Author(s):  
S L Yean ◽  
R J Lin
Keyword(s):  
Mrna Splicing ◽  
Yeast Cells ◽  
Temperature Sensitive ◽  
Small Nuclear Rna ◽  
Small Nuclear Rnas ◽  
Nuclear Rna ◽  
Sensitive Allele ◽  
U4 Rna ◽  
Small Nuclear Ribonucleoproteins

U4 and U6 small nuclear RNAs reside in a single ribonucleoprotein particle, and both are required for pre-mRNA splicing. The U4/U6 and U5 small nuclear ribonucleoproteins join U1 and U2 on the pre-mRNA during spliceosome assembly. Binding of U4 is then destabilized prior to or concomitant with the 5' cleavage-ligation. In order to test the role of U4 RNA, we isolated a functional spliceosome by using extracts prepared from yeast cells carrying a temperature-sensitive allele of prp2 (rna2). The isolated prp2 delta spliceosome contains U2, U5, U6, and possibly also U1 and can be activated to splice the bound pre-mRNA. U4 RNA does not associate with the isolated spliceosomes and is shown not to be involved in the subsequent cleavage-ligation reactions. These results are consistent with the hypothesis that the role of U4 in pre-mRNA splicing is to deliver U6 to the spliceosome.

scholarly journals U4 small nuclear RNA dissociates from a yeast spliceosome and does not participate in the subsequent splicing reaction

1991 ◽  
Vol 11 (11) ◽  
pp. 5571-5577
Author(s):  
S L Yean ◽  
R J Lin
Keyword(s):  
Mrna Splicing ◽  
Yeast Cells ◽  
Temperature Sensitive ◽  
Small Nuclear Rna ◽  
Small Nuclear Rnas ◽  
Nuclear Rna ◽  
Sensitive Allele ◽  
U4 Rna ◽  
Small Nuclear Ribonucleoproteins

U4 and U6 small nuclear RNAs reside in a single ribonucleoprotein particle, and both are required for pre-mRNA splicing. The U4/U6 and U5 small nuclear ribonucleoproteins join U1 and U2 on the pre-mRNA during spliceosome assembly. Binding of U4 is then destabilized prior to or concomitant with the 5' cleavage-ligation. In order to test the role of U4 RNA, we isolated a functional spliceosome by using extracts prepared from yeast cells carrying a temperature-sensitive allele of prp2 (rna2). The isolated prp2 delta spliceosome contains U2, U5, U6, and possibly also U1 and can be activated to splice the bound pre-mRNA. U4 RNA does not associate with the isolated spliceosomes and is shown not to be involved in the subsequent cleavage-ligation reactions. These results are consistent with the hypothesis that the role of U4 in pre-mRNA splicing is to deliver U6 to the spliceosome.

Modifications in small nuclear RNAs and their roles in spliceosome assembly and function

2018 ◽  
Vol 399 (11) ◽  
pp. 1265-1276 ◽  
Author(s):  
Markus T. Bohnsack ◽  
Katherine E. Sloan
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Current Knowledge ◽  
Mrna Splicing ◽  
Cajal Body ◽  
Modified Nucleotides ◽  
Spliceosome Assembly ◽  
Small Nuclear Rnas ◽  
And Function ◽  
Fine Tune

Abstract Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2′-O-methylated nucleotides, which are largely introduced by small Cajal body-specific ribonucleoproteins (scaRNPs). Modified nucleotides typically cluster in functionally important regions of the snRNAs, suggesting that their presence could optimise the interactions of snRNAs with each other or with pre-mRNAs, or may affect the binding of spliceosomal proteins. snRNA modifications appear to play important roles in snRNP biogenesis and spliceosome assembly, and have also been proposed to influence the efficiency and fidelity of pre-mRNA splicing. Interestingly, alterations in the modification status of snRNAs have recently been observed in different cellular conditions, implying that some snRNA modifications are dynamic and raising the possibility that these modifications may fine-tune the spliceosome for particular functions. Here, we review the current knowledge on the snRNA modification machinery and discuss the timing, functions and dynamics of modifications in snRNAs.

scholarly journals m6A mRNA Destiny: Chained to the rhYTHm by the YTH-Containing Proteins

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 49 ◽  
Author(s):  
Ditipriya Hazra ◽  
Clément Chapat ◽  
Marc Graille
Keyword(s):  
Protein Complexes ◽  
Messenger Rnas ◽  
Rna Modifications ◽  
Rna Regulation ◽  
Control Of Gene Expression ◽  
Cellular Processes ◽  
Highly Sensitive ◽  
Yth Domain ◽  
Rna Protein Complexes ◽  
Small Building

The control of gene expression is a multi-layered process occurring at the level of DNA, RNA, and proteins. With the emergence of highly sensitive techniques, new aspects of RNA regulation have been uncovered leading to the emerging field of epitranscriptomics dealing with RNA modifications. Among those post-transcriptional modifications, N6-methyladenosine (m6A) is the most prevalent in messenger RNAs (mRNAs). This mark can either prevent or stimulate the formation of RNA-protein complexes, thereby influencing mRNA-related mechanisms and cellular processes. This review focuses on proteins containing a YTH domain (for YT521-B Homology), a small building block, that selectively detects the m6A nucleotide embedded within a consensus motif. Thereby, it contributes to the recruitment of various effectors involved in the control of mRNA fates through adjacent regions present in the different YTH-containing proteins.

scholarly journals The RNA demethylase FTO targets m6Am in snRNA to establish distinct methyl isoforms that influence splicing

2018 ◽  
Author(s):  
Jan Mauer ◽  
Miriam Sindelar ◽  
Théo Guez ◽  
Jean-Jacques Vasseur ◽  
Andrea Rentmeister ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Mrna Splicing ◽  
Rna Modifications ◽  
Methylation State ◽  
Nucleotide Modification ◽  
Small Nuclear Rnas ◽  
Potential Link ◽  
Endogenous Metabolites

SummarySmall nuclear RNAs (snRNAs) are core spliceosome components and mediate pre-mRNA splicing. During their biogenesis, snRNAs acquire several constitutive nucleotide modifications. Here we show that snRNAs also contain a regulated and reversible nucleotide modification causing them to exist as two different methyl isoforms, m1 and m2, reflecting the methylation state of the adenosine adjacent to the snRNA cap. We find that snRNA biogenesis involves the formation of an initial m1-isoform with a single-methylated adenosine (2’-O-methyladenosine, Am), which is then converted to a dimethylated m2-isoform (N6,2’-O-dimethyladenosine, m6Am). The relative m1- and m2-isoform levels are determined by the RNA demethylase FTO, which selectively demethylates the m2-isoform. We show FTO is inhibited by endogenous metabolites, resulting in increased m2-snRNA levels. Furthermore, cells that exhibit high m2-snRNA levels show altered patterns of alternative splicing. Together, these data reveal that FTO has a central role in snRNA biogenesis and controls a previously unknown step of snRNA processing involving reversible methylation, thereby providing a potential link between reversible RNA modifications and mRNA splicing.

scholarly journals Systemweite Anreicherung von RNA-Protein-Komplexen

BIOspektrum ◽  
2020 ◽  
Vol 26 (6) ◽  
pp. 618-620
Author(s):  
Stefan Pfister ◽  
Benedikt M. Beckmann
Keyword(s):  
Physicochemical Properties ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Rna Metabolism ◽  
Specific Protein ◽  
Cross Linking ◽  
Cell Physiology ◽  
Key Players ◽  
Sequence Elements ◽  
Rna Protein Complexes

Abstract RNA-protein complexes (RNPs) are key players in cell physiology, especially in the context of RNA metabolism. However, their analysis has been dependent on specific protein epitopes or RNA sequence elements, preventing unbiased and cell-wide studies. We developed a three-step protocol, termed Phenol Toluol extraction (PTex), to isolate the complete suite of RNPs in cells, solely based on their unique physicochemical properties after UV-cross-linking. PTex, along with other recently developed unbiased techniques, has the potential to guide the way to cell-wide analysis of RNA-protein interactions.

Structure and Assembly of the Spliceosomal snRNPs

2001 ◽  
Vol 29 (2) ◽  
pp. 15-26 ◽  
Author(s):  
K. Nagai ◽  
Y. Muto ◽  
D. A. Pomeranz Krummel ◽  
C. Kambach ◽  
T. Ignjatovic ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Complexes ◽  
Mrna Splicing ◽  
Protein Recognition ◽  
Conserved Sequences ◽  
X Ray ◽  
Rna Protein Complexes ◽  
Insight Into

The spliceosome is a macromolecular machine that carries out the excision of introns from eukaryotic pre-mRNAs and splicing together of exons. Four large RNA-protein complexes, called the U1, U2, U4/U6 and U5 small nuclear ribo-nucleoprotein particles (snRNPs), and some non-snRNP proteins assemble around three short conserved sequences within the intron in an ordered manner to form the active spliceosome. We aim to provide insight into the molecular details of the mechanism of pre-mRNA splicing through crystallographic studies of the snRNPs. We have solved the X-ray crystal structure of some snRNP proteins as part of either protein-protein complexes or RNA-protein complexes. These structures have provided an important insight into the overall architecture of the U1 and U2 snRNPs and the mechanisms of RNA-protein and protein-protein recognition.

scholarly journals Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production

microLife ◽  
2021 ◽  
Author(s):  
Vanessa Lamm-Schmidt ◽  
Manuela Fuchs ◽  
Johannes Sulzer ◽  
Milan Gerovac ◽  
Jens Hör ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Current Knowledge ◽  
Protein Complexes ◽  
Toxin Production ◽  
Model Organisms ◽  
Gram Positive ◽  
Clostridioides Difficile ◽  
Rna Protein Complexes

Abstract Much of our current knowledge about cellular RNA-protein complexes in bacteria is derived from analyses in gram-negative model organisms, with the discovery of RNA-binding proteins (RBPs) generally lagging behind in gram-positive species. Here, we have applied Grad-seq analysis of native RNA-protein complexes to a major gram-positive human pathogen, Clostridioides difficile, whose RNA biology remains largely unexplored. Our analysis resolves in-gradient distributions for ∼88% of all annotated transcripts and ∼50% of all proteins, thereby providing a comprehensive resource for the discovery of RNA-protein and protein-protein complexes in C. difficile and related microbes. The sedimentation profiles together with pulldown approaches identify KhpB, previously identified in Streptococcus pneumoniae, as an uncharacterized, pervasive RBP in C. difficile. Global RIP-seq analysis establishes a large suite of mRNA and small RNA targets of KhpB, similar to the scope of the Hfq targetome in C. difficile. The KhpB-bound transcripts include several functionally related mRNAs encoding virulence-associated metabolic pathways and toxin A whose transcript levels are observed to be increased in a khpB deletion strain. Moreover, the production of toxin protein is also increased upon khpB deletion. In summary, this study expands our knowledge of cellular RNA protein interactions in C. difficile and supports the emerging view that KhpB homologues constitute a new class of globally acting RBPs in gram-positive bacteria.

Organization of transcription and pre-mRNA splicing within the mammalian cell nucleus

1995 ◽  
Vol 53 ◽  
pp. 768-769
Author(s):  
D.L. Spector ◽  
S. Huang ◽  
S. Kaurin
Keyword(s):  
Rna Polymerase Ii ◽  
Cell Nucleus ◽  
Functional Organization ◽  
Mrna Splicing ◽  
Splicing Factors ◽  
Interchromatin Granule Clusters ◽  
Interchromatin Granule ◽  
Nuclear Regions ◽  
Relationship Of ◽  
Perichromatin Fibrils

We have been interested in the organization of RNA polymerase II transcription and pre-mRNA splicing within the cell nucleus. Several models have been proposed for the functional organization of RNA within the eukaryotic nucleus and for the relationship of this organization to the distribution of pre-mRNA splicing factors. One model suggests that RNAs which must be spliced are capable of recruiting splicing factors to the sites of transcription from storage and/or reassembly sites. When one examines the organization of splicing factors in the nucleus in comparison to the sites of chromatin it is clear that splicing factors are not localized in coincidence with heterochromatin (Fig. 1). Instead, they are distributed in a speckled pattern which is composed of both perichromatin fibrils and interchromatin granule clusters. The perichromatin fibrils are distributed on the periphery of heterochromatin and on the periphery of interchromatin granule clusters as well as being diffusely distributed throughout the nucleoplasm. These nuclear regions have been previously shown to represent initial sites of incorporation of 3H-uridine.

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